Align ABC-type maltose transporter (subunit 3/3) (EC 7.5.2.1) (characterized)
to candidate Ac3H11_1610 Putrescine transport ATP-binding protein PotA (TC 3.A.1.11.1)
Query= BRENDA::P68187 (371 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_1610 Length = 362 Score = 245 bits (626), Expect = 1e-69 Identities = 131/307 (42%), Positives = 195/307 (63%), Gaps = 13/307 (4%) Query: 1 MASVQLQNVTKAWGEVVVSKDINLDIHEGEFVVFVGPSGCGKSTLLRMIAGLETITSGDL 60 M+ +QL +VTK +G + +NL + +GEFV +GPSGCGK+T L+M+AG E +TSG + Sbjct: 1 MSFLQLTDVTKFYGSTCAVQSMNLSVEKGEFVSLLGPSGCGKTTTLQMVAGFEAVTSGRI 60 Query: 61 FIGEKRMNDTPPAERGVGMVFQSYALYPHLSVAENMSFGLKLAGAKKEVINQRVNQVAEV 120 + + + RG+G+VFQSYAL+PH++VA+N+SFGL++ K +R ++VA+ Sbjct: 61 ELAGRDITHAKANTRGLGIVFQSYALFPHMTVADNVSFGLEMRKVPKA---ERKDRVAQA 117 Query: 121 LQLAHL---LDRKPKALSGGQRQRVAIGRTLVAEPSVFLLDEPLSNLDAALRVQMRIEIS 177 L L HL R P+ LSGGQRQRVA+ R LV EP V LLDEPLSNLDA LR +M+ E+ Sbjct: 118 LGLVHLEKHAGRYPRELSGGQRQRVALARALVIEPPVLLLDEPLSNLDAKLREEMQFELR 177 Query: 178 RLHKRLGRTMIYVTHDQVEAMTLADKIVVLDAGRVAQVGKPLELYHYPADRFVAGFIGSP 237 ++ +++G T + VTHDQ EAM+++D++VV++AGR Q+ P +Y +P RF++ F+G Sbjct: 178 QIQRKVGTTTVMVTHDQSEAMSISDRVVVMEAGRATQIDHPHRVYEHPRTRFISTFVG-- 235 Query: 238 KMNFLPVKVTATAIDQVQVELPMPNRQQVWLPVESRDVQVGANMSLGIRPEHLLPSDIAD 297 K N +P +VT + V + + VE + GA + L +RPE L Sbjct: 236 KANLVPGQVTTASATHTHV-----GAGPIEVRVEGAQFRPGAAVLLSVRPEKLQLVPTVQ 290 Query: 298 VILEGEV 304 ++GEV Sbjct: 291 GRIDGEV 297 Lambda K H 0.320 0.137 0.393 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 326 Number of extensions: 9 Number of successful extensions: 2 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 371 Length of database: 362 Length adjustment: 30 Effective length of query: 341 Effective length of database: 332 Effective search space: 113212 Effective search space used: 113212 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 49 (23.5 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory